Medical guidelines aim to provide all professions involved in the treatment of a disease a systematically developed basis for the diagnosis and therapy. They have growing impact on political, juristic and educational issues in Medicine. In Germany, the AWMF (Arbeitsgemeinschaft der Wissenschaftlichen Medizinischen Fachgesellschaften) is responsible for the coordination of the development of medical guidelines. In June 2009 a total of 154 scientific-medical societies constitute the group of members of the AWMF. The German Society for Natural Medicine (Deutsche Gesellschaft für Naturheilkunde) is currently not a member. What is necessary to integrate CAM into medical guidelines? To clarify problems and potential of CAM in medical guidelines, the field of gastroenterology was chosen. In Gastroenterology there are at present 10 S3 guidelines published. Especially inflammatory bowel diseases (IBD) and irritable bowel syndrome (IBS) are diseases that can be very well treated with an integrative medical approach including complementary treatment options. Our work will focus on the experience to integrate CAM made in the development of the recently published guidelines for Crohn's disease as well as the guidelines for ulcerative colitis and irritable bowel syndrome which are presently under development. For the integration of CAM in medical guidelines, more high-quality research in CAM is needed. Furthermore, for the future of Integrative Medicine, it is urgently needed for the German Society for Natural Medicine to become a full member in the AWMF. This will be one major step to ensure and facilitate the inclusion of CAM in medical guidelines in the future, which can be estimated as one important step to further develop Integrative Medicine.